How to remove polyAAA tails with Trimmomatic

Question

[LDT]

Dear all,

I want to remove from my RNAseq data sequences that contain polyA tails. I want to do this via trimmomatic. Did I think about doing it by adding AAAA in the trimming adapter file?

How have others done it?

[ATpoint]

Is this really necessary? How many of these sequences do you have? I guess you run fastqc? It is uncommon to trim polyA in standard RNA-seq.

[LDT]

Hello ATpoint,

I am really curious to find a way to do it. If I remove polyAAA I will ease mapping to the reference. I run fastqc and I see quite often AAAA taking over

[GenoMax]

Aligners can soft clip sequences that do not map so it should not cause a big issue as ATPoint noted.

But to answer your original question yes you could add a fasta formatted poly-A line to your adapters file.